M
Mahmoud Ghandi
Researcher at Broad Institute
Publications - 57
Citations - 14941
Mahmoud Ghandi is an academic researcher from Broad Institute. The author has contributed to research in topics: Cancer & DNA methylation. The author has an hindex of 25, co-authored 54 publications receiving 9010 citations. Previous affiliations of Mahmoud Ghandi include Massachusetts Institute of Technology & Sharif University of Technology.
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Journal ArticleDOI
The Molecular Signatures Database Hallmark Gene Set Collection
Arthur Liberzon,Chet Birger,Helga Thorvaldsdottir,Mahmoud Ghandi,Jill P. Mesirov,Pablo Tamayo +5 more
TL;DR: A combination of automated approaches and expert curation is used to develop a collection of "hallmark" gene sets, derived from multiple "founder" sets, that conveys a specific biological state or process and displays coherent expression in MSigDB.
Journal ArticleDOI
Next-generation characterization of the Cancer Cell Line Encyclopedia
Mahmoud Ghandi,Franklin W. Huang,Franklin W. Huang,Franklin W. Huang,Judit Jané-Valbuena,Judit Jané-Valbuena,Gregory V. Kryukov,Christopher Lo,E. Robert McDonald,Jordi Barretina,Ellen Gelfand,Craig M. Bielski,Haoxin Li,Haoxin Li,Kevin Hu,Alexander Y. Andreev-Drakhlin,Jaegil Kim,Julian M. Hess,Brian J. Haas,François Aguet,Barbara A. Weir,Michael V. Rothberg,Brenton R. Paolella,Michael S. Lawrence,Rehan Akbani,Yiling Lu,Hong L. Tiv,Prafulla C. Gokhale,Antoine de Weck,Ali Amin Mansour,Coyin Oh,Juliann Shih,Kevin Hadi,Yanay Rosen,Jonathan Bistline,Kavitha Venkatesan,Anupama Reddy,Dmitriy Sonkin,Dmitriy Sonkin,Manway Liu,Joseph Lehar,Joshua M. Korn,Dale Porter,Michael D. Jones,Javad Golji,Giordano Caponigro,Jordan E. Taylor,Caitlin M. Dunning,Amanda L. Creech,Allison Warren,James M. McFarland,Mahdi Zamanighomi,Audrey Kauffmann,Nicolas Stransky,Marcin Imielinski,Yosef E. Maruvka,Yosef E. Maruvka,Andrew D. Cherniack,Andrew D. Cherniack,Aviad Tsherniak,Francisca Vazquez,Jacob D. Jaffe,Andrew A. Lane,David M. Weinstock,Cory M. Johannessen,Michael Morrissey,Frank Stegmeier,Robert Schlegel,William C. Hahn,William C. Hahn,Gad Getz,Gordon B. Mills,Jesse S. Boehm,Todd R. Golub,Todd R. Golub,Todd R. Golub,Levi A. Garraway,Levi A. Garraway,William R. Sellers,William R. Sellers +79 more
TL;DR: The original Cancer Cell Line Encyclopedia is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and integration with drug-sensitivity and gene-dependency data, which reveals potential targets for cancer drugs and associated biomarkers.
Journal ArticleDOI
Defining a Cancer Dependency Map
Aviad Tsherniak,Francisca Vazquez,Francisca Vazquez,Phil Montgomery,Barbara A. Weir,Barbara A. Weir,Gregory Kryukov,Gregory Kryukov,Glenn S. Cowley,Stanley Gill,Stanley Gill,William F. Harrington,Sasha Pantel,John M. Krill-Burger,Robin M. Meyers,Levi D. Ali,Amy Goodale,Yenarae Lee,Guozhi Jiang,Jessica Hsiao,William F.J Gerath,Sara Howell,Erin Merkel,Mahmoud Ghandi,Levi A. Garraway,David E. Root,Todd R. Golub,Jesse S. Boehm,William C. Hahn +28 more
TL;DR: DEMETER, an analytical framework that segregates on- from off-target effects of RNAi, demonstrates the basis behind one such predictive model linking hypermethylation of the UBB ubiquitin gene to a dependency on UBC and provides a foundation for a cancer dependency map that facilitates the prioritization of therapeutic targets.
Journal ArticleDOI
Punctuated Evolution of Prostate Cancer Genomes
Sylvan C. Baca,Davide Prandi,Michael S. Lawrence,Juan Miguel Mosquera,Alessandro Romanel,Yotam Drier,Yotam Drier,Kyung Park,Naoki Kitabayashi,Theresa Y. MacDonald,Mahmoud Ghandi,Eliezer M. Van Allen,Eliezer M. Van Allen,Gregory V. Kryukov,Gregory V. Kryukov,Gregory V. Kryukov,Andrea Sboner,Jean-Philippe Theurillat,David Soong,Elizabeth Nickerson,Daniel Auclair,Ashutosh K. Tewari,Himisha Beltran,Robert C. Onofrio,Gunther Boysen,Candace Guiducci,Christopher E. Barbieri,Kristian Cibulskis,Andrey Sivachenko,Scott L. Carter,Gordon Saksena,Douglas Voet,Alex H. Ramos,Alex H. Ramos,Wendy Winckler,Michelle Cipicchio,Kristin G. Ardlie,Philip W. Kantoff,Michael F. Berger,Stacey Gabriel,Todd R. Golub,Matthew Meyerson,Eric S. Lander,Olivier Elemento,Gad Getz,Francesca Demichelis,Francesca Demichelis,Mark A. Rubin,Levi A. Garraway +48 more
TL;DR: In this paper, the genesis of genomic rearrangements, including abundant DNA translocations and deletions that arise in a highly interdependent manner, was modeled and shown to induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution.
Journal ArticleDOI
Genetic and transcriptional evolution alters cancer cell line drug response
Uri Ben-David,Benjamin A. Siranosian,Gavin Ha,Gavin Ha,Helen Tang,Yaara Oren,Yaara Oren,Kunihiko Hinohara,Kunihiko Hinohara,Craig A. Strathdee,Joshua M. Dempster,Nicholas J. Lyons,Robert Burns,Anwesha Nag,Guillaume Kugener,Beth A. Cimini,Peter Tsvetkov,Yosef E. Maruvka,Ryan O’Rourke,Ryan O’Rourke,Anthony J. Garrity,Andrew A. Tubelli,Pratiti Bandopadhayay,Pratiti Bandopadhayay,Aviad Tsherniak,Francisca Vazquez,Bang Wong,Chet Birger,Mahmoud Ghandi,Aaron R. Thorner,Joshua A. Bittker,Matthew Meyerson,Matthew Meyerson,Gad Getz,Gad Getz,Rameen Beroukhim,Todd R. Golub +36 more
TL;DR: The extent, origins and consequences of genetic variation within human cell lines are studied, providing a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.